sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 1.470 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 1.050 | |
| 3w2e | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 1.050 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.984 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.976 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.972 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.959 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.959 | |
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.956 | |
| 1qgy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.956 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.955 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.948 | |
| 3w2f | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.948 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.945 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.941 | |
| 1gr1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.940 | |
| 1w35 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.937 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.937 | |
| 1fnd | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.934 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 0.932 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.930 | |
| 3qft | FAD | NADPH--cytochrome P450 reductase | / | 0.928 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.927 | |
| 1ja1 | FAD | NADPH--cytochrome P450 reductase | / | 0.926 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.916 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.905 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.905 | |
| 1gaw | FAD | Ferredoxin | / | 0.903 | |
| 1e62 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.902 | |
| 1ogj | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.902 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.901 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.901 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.898 | |
| 2pia | FMN | Phthalate dioxygenase reductase | / | 0.894 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.894 | |
| 3ojw | FAD | NADPH--cytochrome P450 reductase | / | 0.894 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.892 | |
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.891 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.891 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.889 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.886 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.885 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.885 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.885 | |
| 4yau | FAD | NADPH--cytochrome P450 reductase | / | 0.875 | |
| 3qfr | FAD | NADPH--cytochrome P450 reductase | / | 0.874 | |
| 1bx0 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.873 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.872 | |
| 1gaq | FAD | Ferredoxin | / | 0.867 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.865 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.863 | |
| 4yao | FAD | NADPH--cytochrome P450 reductase | / | 0.862 | |
| 1cqx | FAD | Flavohemoprotein | / | 0.856 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.856 | |
| 3zbt | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.853 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.852 | |
| 2xnc | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.847 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.844 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.843 | |
| 3ojx | FAD | NADPH--cytochrome P450 reductase | / | 0.841 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.833 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.832 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.827 | |
| 1sm4 | FAD | Ferredoxin--NADP reductase | / | 0.824 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.822 | |
| 1qgz | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.818 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.813 | |
| 2bpo | FAD | NADPH--cytochrome P450 reductase | / | 0.812 | |
| 1b2r | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.808 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.805 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.802 | |
| 3w5u | FAD | Ferredoxin | / | 0.799 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.796 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.794 | |
| 4k1x | FAD | NADPH:ferredoxin reductase | / | 0.792 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.780 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.779 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.767 | |
| 5cho | FAD | Flavin reductase | / | 0.762 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.761 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.760 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.755 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.752 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.747 | |
| 5j4e | FMN | Sensory box protein | / | 0.747 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.746 | |
| 1ty9 | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.745 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.745 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.741 | |
| 4yaf | FAD | NADPH--cytochrome P450 reductase | / | 0.738 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.737 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.735 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.731 | |
| 5j3w | FMN | Sensory box protein | / | 0.731 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.721 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.719 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.717 | |
| 2ard | FDA | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.716 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.705 | |
| 1wlk | FMN | FMN-binding protein | / | 0.704 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.704 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.703 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.703 | |
| 1eje | FMN | Protein MTH_152 | / | 0.700 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.699 | |
| 3a6q | FMN | FMN-binding protein | / | 0.696 | |
| 3a6r | FMN | FMN-binding protein | / | 0.696 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.696 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.695 | |
| 1n07 | FMN | Riboflavin kinase | 2.7.1.26 | 0.694 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.694 | |
| 4l82 | FMN | Uncharacterized protein | / | 0.693 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.693 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.692 | |
| 2nr4 | FMN | Conserved protein | / | 0.691 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.690 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.689 | |
| 1flm | FMN | FMN-binding protein | / | 0.687 | |
| 1usc | FMN | Monooxygenase | / | 0.686 | |
| 2ou5 | FMN | Pyridoxamine 5'-phosphate oxidase-related FMN-binding protein | / | 0.686 | |
| 2e83 | FMN | FMN-binding protein | / | 0.684 | |
| 3a20 | FMN | FMN-binding protein | / | 0.684 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.684 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.683 | |
| 3pft | FMN | Flavin reductase | / | 0.683 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.682 | |
| 2wes | FAD | Tryptophan 5-halogenase | / | 0.681 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.681 | |
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 | 0.680 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.680 | |
| 2aqj | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.680 | |
| 4hj4 | FMN | LOV protein | / | 0.680 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.679 | |
| 4gde | FDA | UDP-galactopyranose mutase | / | 0.679 | |
| 4u8m | FDA | UDP-galactopyranose mutase | / | 0.679 | |
| 5hy5 | FAD | Tryptophan 6-halogenase | / | 0.678 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.676 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.675 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.675 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.673 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.672 | |
| 2wet | FAD | Tryptophan 5-halogenase | / | 0.671 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.670 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.669 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.668 | |
| 4hnb | FMN | LOV protein | / | 0.668 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.666 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.665 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.664 | |
| 3of4 | FMN | Nitroreductase | / | 0.664 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.664 | |
| 3vy5 | FMN | FMN-binding protein | / | 0.664 | |
| 4u8p | FDA | UDP-galactopyranose mutase | / | 0.664 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.663 | |
| 3awh | FMN | FMN-binding protein | / | 0.663 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.662 | |
| 3amf | FMN | FMN-binding protein | / | 0.662 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.662 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.660 | |
| 4aut | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.660 | |
| 3bnk | FMN | Flavoredoxin | / | 0.659 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.659 | |
| 1wli | FMN | FMN-binding protein | / | 0.658 | |
| 2cul | FAD | GidA-related protein | / | 0.658 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.657 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.657 | |
| 3sw1 | FMN | Sensory box protein | / | 0.657 | |
| 1ci0 | FMN | Pyridoxamine 5'-phosphate oxidase | 1.4.3.5 | 0.656 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.656 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.655 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.654 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.654 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.653 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.652 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.651 | |
| 4feh | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.651 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.650 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.650 |